Biochemical Genetics最新文献

{"title":"Quantitative Trait Locus Mapping and Candidate Gene Analysis of the Contents of Three Tanshinone Components in Salvia miltiorrhiza Bunge.","authors":"Yan Yu, Zaijun Yang, Yichao Wu, Yuanyuan Jiang, Jinqiu Liao, Ruiwu Yang, Li Zhang","doi":"10.1007/s10528-024-10964-6","DOIUrl":"https://doi.org/10.1007/s10528-024-10964-6","url":null,"abstract":"<p><p>Tanshinones are abietane diterpenoid quinone compounds with diverse biological activities and pharmacological effects found in Salvia miltiorrhiza. Leveraging the high-density genetic map established through our prior research endeavors, we conducted a quantitative trait locus (QTL) analysis pertaining to the concentrations of three major tanshinone components, cryptotanshinone, tanshinone I, and tanshinone IIA, in S. miltiorrhiza. This extensive investigation was conducted across three distinct planting environments, ultimately identifying a comprehensive repertoire of 27 discernible QTLs. These QTLs were mapped onto four distinct linkage groups (LG), namely LG1, LG5, LG6, and LG7, which explained 3.11%-37.85% phenotypic variation. Candidate genes were projected based on consistent QTLs detected for each active ingredient in three environments. Nineteen putative candidate genes involved in the regulation of tanshinone biosynthesis were identified. These genes participate in primary metabolic and multiple branching terpenoid biosynthesis pathways, forming a complex regulatory network. Our findings have the potential to offer novel insights into advancing the understanding of the regulatory mechanisms governing tanshinone biosynthesis. Furthermore, these results establish crucial groundwork for gene discovery, marker-assisted selection breeding, and map-based cloning of functional genes associated with tanshinone content in S. miltiorrhiza.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Meta-Analysis of Association Between Interleukin Polymorphisms (rs4073, rs1800925, rs1179251, rs1179246, rs2227485, rs17855750, and rs153109) and Colorectal Cancer Risk.","authors":"Sepehr Sadafi, Nasrin Amirifard, Omid Emami Aleagha, Seyed Ghasem Mirbahari, Masoud Sadeghi","doi":"10.1007/s10528-024-10969-1","DOIUrl":"https://doi.org/10.1007/s10528-024-10969-1","url":null,"abstract":"<p><p>Interleukins (ILs) play a significant role in triggering the inflammatory response in blood vessels and immune cells. A systematic review and meta-analysis were conducted to investigate the relationship between IL-8 (rs4073), IL-13 (rs1800925), IL-22 (rs1179251, rs1179246, and rs2227485), and IL-27 (rs17855750 and rs153109) polymorphisms and the risk of developing colorectal cancer (CRC). Four databases were searched up until October 13, 2023, without any restrictions, to find relevant studies. The association was evaluated using crude odds ratios (ORs) and 95% confidence intervals in five genetic models. A total of twenty-three articles were entered into the meta-analysis. The pooled ORs (p-values) for the IL-8 (rs4073) polymorphism were 0.98 (0.63), 0.93 (0.44), 0.89 (0.13), 0.94 (0.38), and 0.99 (0.90) for studies following HWE without heterogeneity, and for all studies with high heterogeneity were 1.03 (0.69), 1.30 (0.07), 1.04 (0.71), 1.12 (0.20), and 1.23 (0.06). For the IL-13 (rs1800925) polymorphism, the pooled ORs were 1.44 (0.06), 2.58 (0.0004), 1.72 (0.16), 1.82 (0.09), and 2.37 (0.001) in AHHDR models, respectively. The pooled ORs of IL-22 (rs1179251) polymorphism for AHHDR models were 0.97 (0.92), 0.92 (0.90), 0.98 (p = 0.95), 1.08 (0.87), and 0.96 (0.82), respectively. The pooled ORs of IL-22 (rs1179246) polymorphism for AHHDR models were 0.98 (0.67), 0.97 (0.80), 0.92 (0.36), 0.93 (0.42), and 1.02 (0.84), respectively. The pooled ORs of IL-22 (rs2227485) polymorphism for AHHDR models were 1.47 (0.02), 2.03 (0.02), 1.28 (0.29), 1.52 (0.06), and 1.70 (0.04), respectively. The pooled ORs of IL-27 (rs17855750) polymorphism for AHHDR models were 0.53 (0.46), 0.19 (0.28), 1.10 (0.60), 0.55 (0.58), and 0.27 (p = 0.05), respectively. The pooled ORs of IL-27 (rs153109) polymorphism for AHHDR models were 1.28 (0.007), 1.45 (0.002), 1.40 (0.0002), 1.41 (< 0.0001), and 1.20 (0.09), respectively. The results reported that just the TT genotype of IL-13 (rs1800925), the T allele and TT genotype of IL-22 (rs2227485), and the G allele and GG, AG and GG + AG genotypes of IL-27 (rs153109) polymorphisms had an elevated risk in CRC patients.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Codon Usage Pattern and its Influencing Factors for Mitochondrial CO Genes Among Different Subfamilies of Cerambycidae.","authors":"Yuyang Zhang, Huanxi Yu, Buddhi Dayananda, Tao Yu","doi":"10.1007/s10528-024-10967-3","DOIUrl":"https://doi.org/10.1007/s10528-024-10967-3","url":null,"abstract":"<p><p>This study examined nucleotide composition and codon usage of mitochondrial CO (cytochrome oxidase) genes from four subfamilies of Cerambycidae. Nucleotide composition analysis of the CO genes revealed an AT-rich pattern in the four subfamilies of Cerambycidae. Furthermore, by analyzing the correlation between the overall nucleotide composition of CO genes and the nucleotide composition of the 3rd codon, we found that mutation pressure and natural selection were the key factors affected the CUB. The regression of GC12 (The average of GC content of the entire gene first and second codon positions) vs GC3 (GC content of the entire gene third codon positions) scattered to a limited value, and all CO genes slope of the regression line was all less than 0.5, indicated that natural selection might have played a significant role in shaping the codon usage bias. ENC plot analysis further supported the predominant influence of natural selection on CUB, aligning with the findings from neutral plot analyses. These novel insights into the codon evolution of CO genes within Cerambycidae significantly contribute to our understanding of codon evolution.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary Analysis of the hnRNP Interactomes and Their Functions in Eukaryotes.","authors":"M J Nishanth, Shanker Jha","doi":"10.1007/s10528-024-10956-6","DOIUrl":"https://doi.org/10.1007/s10528-024-10956-6","url":null,"abstract":"<p><p>The heterogeneous nuclear ribonucleoproteins (hnRNPs) are central regulators of several fundamental biological processes across eukaryotes. hnRNPs have been implicated in transcriptional and post-transcriptional regulation, telomere maintenance, stem cell maintenance, among other processes in major model organisms. Though hnRNPs are known to be conserved in eukaryotes, the evolutionary conservation/diversification of their functions across species is yet to be understood. To this end, the present work employed computational analyses to identify potential hnRNP orthologs in eighty eukaryotic species, and their interactors. Subsequently, a comprehensive analysis of the biological processes influenced by hnRNP interactomes showed alternative splicing and splicing regulation to be commonly associated with most species, while a few processes were uniquely associated with particular species. Further studies of the clustering patterns of the top-ranking hub nodes of the hnRNP protein networks revealed a notable clustering pattern of hnRNP K orthologs from five species. Subsequent analysis of the genes with overrepresented hnRNP K target sites within their untranslated regions showed hnRNP K orthologs from humans and Ciona intestanilis to potentially target transcripts involved in membrane-related processes. Remarkably, the hnRNP K ortholog from Lottia gigantea was found to possibly regulate other RNA-binding proteins (RBPs), suggesting a regulatory cascade involving hnRNPs and other RBPs. Further experimental studies in this regard would be of scientific and clinical importance, owing to the druggability of several human hnRNPs.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression Levels of PF4, ALOX12, ITGA2B, F131A in Pregnant COVID-19 Survivors.","authors":"Mai M Shaker, Asia E Abdelghany, Nesma M Elaraby","doi":"10.1007/s10528-024-10958-4","DOIUrl":"10.1007/s10528-024-10958-4","url":null,"abstract":"<p><p>COVID-19 is viral illness caused by SARS-CoV-2. The immediate complications of COVID-19 are well defined and associated with increased mortality. A global effort is required to determine its effects on implantation, fetal growth and labor. Post COVID-19 recovery period presents a further challenge regarding service provision, prevention, and management. To assess the expression of Platelet Factor 4 (PF4), Arachidonate 12-lipoxygenase (ALOX 12), Integrin alpha-IIb (ITGA2B) & Coagulation Factor XIII A Chain F13A1 in post-acute COVID-19 survivors pregnant women. Prospective case control study, conducted on 400 pregnant women. Case group consists of 200 singleton pregnancies who had recovered from COVID-19 since 4-6 weeks before conception. Control group consists of 200 singleton pregnancies with no history for COVID-19. Expression levels of ALOX12, PF4, ITGA2B, and F13A1genes were determined using quantitative reverse transcription polymerase chain reaction method (qRT-PCR). Expression levels of ALOX12, ITGA2B, and F13A1, were significantly higher in the patients group (3.82±9.6, 6.63±8.45, and 8.9±9.1, respectively) (p < 0.05) compared to those in the control group (1.0±6.0, 1.0±8.1, and 0.6±7.6, respectively). No significant difference in PF4 expression between patients and control group (p = 0.3). Results obtained from enrichment analysis have also supported the above findings. Relative expression levels of these candidate genes could be distinguished between post-acute COVID-19 survivors' pregnant women and control group, significant relative gene expression of ALOX12, ITGA2B, and F13A1 may be associated with an increased risk of placenta-mediated adverse pregnancy outcomes.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The LINC01094/miR-545-3p/SLC7A11 Signaling Axis Promotes the Development of Gastric Cancer by Regulating Cell Growth and Ferroptosis.","authors":"Hui Wang, Chao Li, Song Meng, Yu-Ting Kuang","doi":"10.1007/s10528-024-10959-3","DOIUrl":"https://doi.org/10.1007/s10528-024-10959-3","url":null,"abstract":"<p><p>This study aimed to investigate the role and mechanism of action of LINC01094 in the development of gastric cancer (GC). The expression levels of LINC01094 in GC patients and healthy individuals were analyzed online using the Cancer Genome Atlas database. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot analyses were performed to determine the expression of LINC01094/miR-545-3p/SLC7A11 in GC tissues and cells. Functional experiments (MTT assay, colony formation assay, and flow cytometry) were conducted to assess the effect of LINC01094 and miR-545-3p on cell proliferation, viability, apoptosis, cell cycle, and reactive oxygen species. Correlations between LINC01094 and miR-545-3p, as well as SLC7A11, were analyzed and validated using the dual-luciferase reporter assay and RNA immunoprecipitation. The levels of Fe²⁺, malondialdehyde, and glutathione in the cells were measured biochemically, and the protein expression levels of Bcl-2, cleaved caspase3, Cyclin D1, and p21 were detected by Western blotting. LINC01094 was significantly upregulated in the GC tissues and cells with a targeting relationship with miR-545-3p; the expression levels of LINC01094 and miR-545-3p were negatively correlated. Knockdown of LINC01094 notably inhibited the proliferation and viability of GC cells and promoted cell ferroptosis, which, however, was abrogated by the silencing of miR-545-3p. These findings indicate that miR-545-3p could target and positively correlate with SLC7A11 expression. Additionally, LINC01094 could promote GC cell progression and affect cellular ferroptosis by regulating the miR-545-3p/SLC7A11 signaling axis.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancing Chickpea Breeding: Omics Insights for Targeted Abiotic Stress Mitigation and Genetic Enhancement.","authors":"Muhammad Tanveer Altaf, Waqas Liaqat, Amjad Ali, Amna Jamil, Muhammad Fahad, Muhammad Aneeq Ur Rahman, Faheem Shehzad Baloch, Heba I Mohamed","doi":"10.1007/s10528-024-10954-8","DOIUrl":"https://doi.org/10.1007/s10528-024-10954-8","url":null,"abstract":"<p><p>Chickpea is a major source of proteins and is considered the most economically vital food legume. Chickpea production is threatened by several abiotic and biotic factors worldwide. The main constraints limiting worldwide chickpea production are abiotic conditions such as drought, heat, salinity, and cold. It is clear that chickpea is treasured for its nutritive value, in particular its high protein content, and hence study of problems like drought, cold and salinity stresses are very important concerning chickpeas. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. The most crippling economic losses in agriculture occur due to these abiotic stressors, which affect plants in many ways. All these abiotic stresses affect the water relations of the plant, both at the cellular level as well as the whole-plant level, causing both specific and non-specific reactions, damage and adaptation reactions. These stresses share common features. Breeding programs use a huge collection of over 100,000 chickpea accessions as their foundation. Significant advancements in conventional breeding, including mutagenesis, gene/allele introgression, and germplasm introduction, have been made through this method. Abiotic tolerance and yield component selection are made easier by creating unique DNA markers for the genus Cicer, which has been made possible by developments in high-throughput sequencing and molecular biology. Transcriptomics, proteomics, and metabolomics have also made it possible to identify particular genes, proteins, and metabolites linked to chickpea tolerance to abiotic stress. Chickpea abiotic stress tolerance has been directly and potentially improved by biotechnological applications, which are covered by all 'Omics' approaches. It requires information on the abiotic stress response at the different molecular levels, which comprises gene expression analysis for metabolites or proteins and its impact on phenotype. Studies on chickpea genome-wide expression profiling have been conducted to determine important candidate genes and their regulatory networks for abiotic stress response. This study aimed to offer a detailed overview of the diverse 'Omics' approaches for resilience's to abiotic stresses on chickpea plants.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing Genomic DNA Extraction from Avian Feathers: A Modified Phenol-Chloroform Approach for Enhanced Efficiency and Cost-Effectiveness.","authors":"Demir Ozdemir, Leyla Bener, Emine Toparslan Akcay","doi":"10.1007/s10528-024-10957-5","DOIUrl":"https://doi.org/10.1007/s10528-024-10957-5","url":null,"abstract":"<p><p>The procurement of blood and tissue samples for DNA extraction in avian species intended for molecular studies is associated with the induction of discomfort and pain in the subjects, compounded by practical challenges in application and ethical considerations. Consequently, feathers have emerged as a more prevalent source for molecular investigations, particularly in the fields of poultry and ornithology. However, the effective extraction of DNA from feathers necessitates the breakdown of the hard keratinized tissue within the feather structure. This study aimed to devise a highly efficient, cost-effective, and easily adaptable Modified Phenol-Chloroform (MPC) approach for genomic DNA extraction from feathers, addressing shortcomings identified in previous studies on feather-based DNA isolation. The MPC method was employed to extract genomic DNA from feather samples obtained from six distinct avian species (chicken, guinea fowl, canary, pigeon, emu, and goose). Comparative evaluation of DNA isolation efficiency was conducted by employing two different commercial DNA kits alongside the MPC method. The results showed significantly higher DNA concentrations (ng/ml) from chicken feathers using the MPC method compared to those obtained with commercial kits (p < 0.05), along with high DNA purity (1.83 ± 0.11). Subsequent PCR experiments, employing nuclear and mitochondrial DNA-specific primers, illustrated the effective amplification of short and long fragments from MPC-isolated DNA samples. In contrast to commercial kits, the findings underscore the successful application of the MPC method in isolating high-quality genomic DNA from feathers characterized by elevated keratin content.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Causality Between Immune Cells, Metabolites and Breast Cancer: Mendelian Randomization and Mediation Analysis.","authors":"Changlong Wei, Changwang Li, Gongyin Zhang, Honghui Li, Jingsong Li, Jinsheng Zeng","doi":"10.1007/s10528-024-10966-4","DOIUrl":"https://doi.org/10.1007/s10528-024-10966-4","url":null,"abstract":"<p><p>Previous studies have shown that immune cells and metabolites are associated with the development of breast cancer, but the causal relationship is unclear. We use Mendelian randomization (MR) to explore potential connections between them. Based on two sample MR studies, we evaluated the causal relationship between 731 immune cell traits, 1400 metabolites and breast cancer. In addition, we evaluated the mediating role of metabolites between immune cells and breast cancer using two-step MR Studies. Pooled GWAS data on 731 immune cell traits (n = 3757), 1400 metabolites (n = 8299) and breast cancer (ncase = 122,977, ncontrol = 105,974) were obtained from publicly available authoritative databases. We mainly used inverse variance weighted (IVW) method combined with Bayesian weighted MR (BWMR), MR-Egger, weighted median, simple mode, and weighted mode methods. The results of MR Studies showed that 3 immune cells and 15 metabolites were associated with an increased risk of breast cancer. 8 immune cells and 11 metabolites are associated with a reduced risk of breast cancer. Mediating MR Analysis showed that 6 metabolites, Tricosanoyl sphingomyelin (d18:1/23:0) levels(Mediated proportion:17.5%), N-palmitoyl-heptadecasphingosine (d17:1/16:0) levels(8.74%), Inosine 5'-monophosphate (IMP) to phosphate ratio(11.3%), Glutamine to asparagine ratio(5.43%), Oleoyl-linoleoyl-glycerol (18:1/18:2) [2] levels(8.48%), and Sphinganine-1-phosphate levels(8.68%), were found to mediate the relationship between immune cells and breast cancer. Our study reveals a potential causal relationship among multiple immune cells traits, metabolites, and breast cancer. It provides valuable clues and potential therapeutic targets for breast cancer biomarker discovery and breast cancer treatment.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During the Peak of the Pandemic in Türkiye.","authors":"Faruk Berat Akçeşme, Tuğba Kul Köprülü, Burçin Erkal Çam, Şeyma İş, Birsen Cevher Keskin, Betül Akçeşme, Kürşad Nuri Baydili, Bahar Gezer, Jülide Balkan, Bihter Uçar, Osman Gürsoy, Mehmet Taha Yıldız, Halil Kurt, Nevzat Ünal, Celalettin Korkmaz, Özlem Bayraktar Saral, Barış Demirkol, Yasemin Çağ, Hilal Abakay, Şükran Köse, Hasan Türkez, Kenan Çadırcı, Mustafa Altındiş, Yasemin Derya Gülseren, Nuray Aslan, Abdulkadir Özel, Muhammet Atıf Karagöl, Neslihan Mutluay, Şaban Tekin","doi":"10.1007/s10528-024-10962-8","DOIUrl":"https://doi.org/10.1007/s10528-024-10962-8","url":null,"abstract":"<p><p>SARS-CoV-2 is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease. Genomic characterization of SARS-CoV-2 is important for monitoring and assessing its evolution. A total of 1.346 nasopharyngeal swab samples were collected but only 879 SARS-CoV-2 high-quality genomes were isolated, subjected to Next Generation Sequencing and analyzed both statistically and regarding mutations comprehensively. The distribution of clades and lineages in different cities of Türkiye and the association of SARS-CoV-2 variants with age groups and clinical characteristics of COVID-19 were also examined. Furthermore, the frequency of the clades and lineages was observed in 10 months. Finally, non-synonymous mutations not defined in specific SARS-CoV-2 variants (during that period) were identified by performing mutation analysis. B.1.1.7 (Alpha) and B.1.617.2 (Delta) SARS-CoV-2 variants which have also been identified in our study from March to December 2021. We observed a significant association of SARS-CoV-2 variants with age groups and cities. Also, E:T9I, S:A27S, S:A67V, S:D796Y, S:K417N, S:N440K, S:R158X, S:S477N (below 1%-frequency) were determined as specific mutations belonging and shared with the Omicron variant that appeared later. Our study has highlighted the importance of constant monitoring of the genetic diversity of SARS-CoV-2 to provide better prevention strategies and it contributes to the understanding of SARS-CoV-2 from the past to the present.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}